February 16, 2013

Higher Levels of Neanderthal Ancestry in East Asians Than in Europeans (Wall et al. 2013)

The title seems to say it all; such a conclusion was also arrived at by Meyer et al.(high coverage Denisova paper). However, the extent of this ancestry appears to be differently estimated in the new paper:

By using the high coverage Denisova genome, we are able to show that the admixture rate into East Asians is 40% higher than into Europeans.

Of course, the interesting question is why East Asians have this excess of Neandertal ancestry, given that Neandertals were a west Eurasian-distributed species (for the most part). Similarly, we would not have expected Australo-Melanesians to possess higher Denisovan admixture, and yet they do. Some models of multiregional evolution assumed regional continuity with pre-existing archaic populations in different parts of the world (e.g., Europeans with Neandertals), but clearly much more interesting things were taking place in deep prehistory.

Of particular interest is this conclusion:

In particular, at least some Neanderthal-modern human admixture must postdate the separation of the ancestors of modern European and modern East Asian populations.

The publication of Tianyuan has shown that by ~40kya, differentiation of Asians from Europeans was already on its way, and this is a date close to the disappearance of the Neandertals, the date of which is contested, but one can imagine that already-differentiated Eurasians may have encountered some lingering Neandertal groups.

Genetics doi: 10.1534/genetics.112.148213

Higher Levels of Neanderthal Ancestry in East Asians Than in Europeans

Jeffrey D. Wall et al.

Neanderthals were a group of archaic hominins that occupied most of Europe and parts of Western Asia from roughly 30-300 thousand years ago (Kya). They coexisted with modern humans during part of this time. Previous genetic analyses that compared a draft sequence of the Neanderthal genome with genomes of several modern humans concluded that Neanderthals made a small (1-4%) contribution to the gene pools of all non-African populations. This observation was consistent with a single episode of admixture from Neanderthals into the ancestors of all non-Africans when the two groups coexisted in the Middle East 50-80 Kya. We examined the relationship between Neanderthals and modern humans in greater detail by applying two complementary methods to the published draft Neanderthal genome and an expanded set of high-coverage modern human genome sequences. We find that, consistent with the recent finding of Meyer et al. (2012), Neanderthals contributed more DNA to modern East Asians than to modern Europeans. Furthermore we find that the Maasai of East Africa have a small but significant fraction of Neanderthal DNA. Because our analysis is of several genomic samples from each modern human population considered, we are able to document the extent of variation in Neanderthal ancestry within and among populations. Our results combined with those previously published show that a more complex model of admixture between Neanderthals and modern humans is necessary to account for the different levels of Neanderthal ancestry among human populations. In particular, at least some Neanderthal-modern human admixture must postdate the separation of the ancestors of modern European and modern East Asian populations.

12 comments:

The Neanderthal admixture in the Maasi is surely due to back migration of Eurasians who participated in Maasi ethnogenesis or introgressed into their gene pool later.

One model that makes sense would be an initial admixture event of all proto-modern humans in the Levant or elsewhere in SW Asia, followed by schism with the proto-Asians going to India and experiencing subsequent admixture specific to them enroute or in South Asia.

There is further admixture in Europe with Cro-Magnon West Eurasians as well. But this secondary admixture is greatly diluted by subsequent waves of modern humans from SW Asia (who had only the initial Levantine/SW Asian wave of admixture) during the repopulation of Europe after the Last Glacial Maximum, during the Neolithic and during the early Metal Ages (by the end of which the currently European population genetic makeup was mostly in place) that the second wave of Neanderthal admiture acquired by European Cro-Magnons was diluted to levels lower than the additional quantum of Neadnerthal admixture that the proto-Asians picked up en route to India.

The model is then modified to provide that there is one instance of Denisovan admixture on the Flores side of the Wallace line ca. 45-50kya, probably with H. Florensis (interpreted as a local dwarf variant of whatever archaic hominin species the Denisovans belonged to at the extreme of what was once a much wider geographic range possibly with a hole in the middle of it caused by the Toba explosion), since that is a case where there was a well documented period of co-existence between archaic hominins and modern humans in which both must have had fairly modest effective populations. The Siberian Denisovans in this model are a relict population (possibly admixed as well) with origins in Southern route Asia. This fits the geographic distribution of the genetic traces of this admixture and is well placed to explain how this could arise from founder effects in both Papuans and aboriginal Australians. Asian archaic hominins may have been less similar to modern humans than Neanderthals were, so admixture rates with them on the other side of the Wallace line may have been lower outside the perfect storm conditions of Flores and was largely lost to genetic drift and/or diluted to trace levels by subsequent waves of populations that arrived after the extinction of archaics in mainland Asia.

It would be interesting to see if populations with higher proportions of mtDNA N derived haplogroups and Y-DNA haplogroup F derived haplogroups (found in both West and East Eurasia) have as one might suspect given the lower levels of Neanderthal admixture in West Eurasians, lower levels of Neanderthal admixture than populations with higher proportions of mtDNA M derived haplogroups and Y-DNA C and D derived haplogroups (mostly absent in West Eurasia except a backmigrating M1).

The explanation for the discrepancy of higher Neanderthal ancestry in East Asian compared with Europeans could be simple. Europeans, West Eurasians generally have closer genetic ties with Africans which East Asians generally do not. The greater and more recent genetic contribution of Africans to the European and West Eurasian genepool would of necessity, lower the contributions made by Neanderthals in the past admixture events just as people of mostly West Eurasian ancestry with significant African ancestry generally will have lower Neanderthal ancestry detectable by these tests.

Imagine that a pack of wolves and a pack of Pekingese produce a race of wolf-Pekingese hybrids. Then imagine that a herd of "scientists" sequence the wolf genome, the Doberman genome, and the wolf-Pekingese hybrid genome, and then go on and on for years about how the wolf-Pekingese hybrids are wolf-Doberman hybrids. Pretty stupid, huh?

Didn't Europeans also largely originate from the sub-continent (including ~Pakistan) and from SE and pre-mongoloid C/E Asia? As far as I can tell, there is zero evidence for Europeans originating outside that region. So, any additional Asian Neanderthal admixture must have been an additional event, and - as I have always said - the most likely candidate is an earlier (the earliest) AMH migration eastward associated with y-DNA haplogroup D.

Also, what evidence is there that people from SW Asia diluted European autosomal DNA to any significant extent during the three periods you mentioned? Outside of the extreme SE Europe (largely, Greece and immediately adjacent Balkans) and a tiny amount along the Mediterranean cost (which actually may be y-DNA only, virtually without autosomal), I see no such evidence, at all.

These people are going to look really stupid when the first eastern heidelbergensis sequences come out.

geneticer,

I wouldn't quite go that far, but yes; we currently don't know the exact relationship between heidelbergensis, Denisovans, and erectus. Part of both eastern "Neanderthal" and "Densisovan" admixtures could in reality be heidelbergensis and erectus admixture events.

Current estimates of African admixture in Southern Europeans is in the single digit or low double digit percentages at present, which shouldn't be large enough to cause the differences observed. But, these estimates implicitly ignore admixture that gives rise in the first place to the staistically inferred proto-West Eurasian ancestral DNA profile from which African DNA is being distinguished in these estimates. And, Upper Paleolithic NE African population genetics may have been more similar to West Eurasian population genetics then than they are now.

I am quite comfortable in stating that there is not enough evidence to be sure what demographic and migration history underlies the West Eurasian v. East Eurasian differentition in population genetics.

We know from Y-DNA, mtDNA, autosomal genetics and archaic admixture evidence (both in terms of a different mix of particular Neanderthal SNPs in West v. East Eurasians and in different overall frequencies and in Denisovan admixture) that the first order split within Eurasians is between West Eurasians and East Eurasians.

We can place some boundries on the latest dates at which this differentiation could have happened (ca. 40 kya and post-Out of Africa ca. 100kya to 125 kya).

It is fair to assume that this population genetic differentiation between West Eurasians and East Eurasians took place geographically someplace between Burma and the Balkans and the far Northeastern African fringe where it borders SW Asia.

It is fair to assume that this divide arose sometime before the ancestral West Eurasian Y-DNA and mtDNA haplogroups reached population genetic fixation frequencies in an ancestral Eurasian population that had both West Eurasian and East Eurasian uniparental haplogroups (it is unappreciated that the divide is too stark to have arisen from founder effect in a fully mixed population that has already reached population genetic fixation with plausibly sized founder populations). At some point in time there had to be a proto-West Eurasian population that included only a subset of the genetic diversity now found in East Eurasians.

But, the process that brought this first order divide in DNA variation about is otherwise very speculative. To the extent that there has since been nearly complete population replacement in SW Asia from the Out of Africa to Out of Arabia era (and everyone agrees that there were Eurasians in Arabia but not elsewhere for some period of time), this could be a case where an absence of evidence is misleading.

"what evidence is there that people from SW Asia diluted European autosomal DNA to any significant extent during the three periods you mentioned?"

Otzi the Iceman's high level of Neanderthal admixture is the strongest piece of evidence.

There is some less definitive but direct evidence from European hunter-gather physical anthropology in the direction of Neanderthal traits, taken together with the known existence of some admixture between the two species.

Dilution of Cro-Magnon DNA by SW Asian or W Asian DNA is definitively established by the dramatic shift in ancient DNA frequencies at the Neolithic boundary in mtDNA haplogroups and between then and the present; archaeology and physical anthropology coroborate this ancient DNA evidence. This dilution was something on the order of 4-1 to 9-1 ratios of SW Asian/W Asian migrant derived DNA haplogroups to Cro-Magnon derived DNA haplogroups (+/- perhaps 50%). So, if Cro-Magnon DNA from ca. 29 kya when Neanderthals went extinct to 10 kya at the start of the Holocene migrations was elevated, their DNA would have been diluted.

At some point in time there had to be a proto-West Eurasian population that included only a subset of the genetic diversity now found in East Eurasians.

Andrew,

However, extant Europeans have similar levels of genetic diversity as East Asians.

Dilution of Cro-Magnon DNA by SW Asian or W Asian DNA is definitively established by the dramatic shift in ancient DNA frequencies at the Neolithic boundary in mtDNA haplogroups and between then and the present; archaeology and physical anthropology coroborate this ancient DNA evidence. This dilution was something on the order of 4-1 to 9-1 ratios of SW Asian/W Asian migrant derived DNA haplogroups to Cro-Magnon derived DNA haplogroups (+/- perhaps 50%).

West Asian - yes. SW Asian? I don't think so (outside of extreme SE Europe). Also, your estimates for replacement are way too high, especially for northern Europeans (who, autosomally, are more HGs than later arrivals).

Finally, Gravettian was the last pan-European culture before LGM, so I would assume that European paleolithic haplotypes and autosomal DNA got fixed during that time - not with Cro-Magnons.

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